David F. Savage - Publications

University of California, Berkeley, Berkeley, CA 
Biophysics, Synthetic Biology, and Systems Biology

30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Huang TP, Zhao KT, Miller SM, Gaudelli NM, Oakes BL, Fellmann C, Savage DF, Liu DR. Author Correction: Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nature Biotechnology. PMID 31182863 DOI: 10.1038/s41587-019-0168-1  0.52
2019 Huang TP, Zhao KT, Miller SM, Gaudelli NM, Oakes BL, Fellmann C, Savage DF, Liu DR. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nature Biotechnology. PMID 31110355 DOI: 10.1038/s41587-019-0134-y  0.52
2019 Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nature Communications. 10: 2127. PMID 31073154 DOI: 10.1038/s41467-019-09985-2  0.52
2019 Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell. 176: 254-267.e16. PMID 30633905 DOI: 10.1016/j.cell.2018.11.052  0.52
2016 Gerhardt KP, Olson EJ, Castillo-Hair SM, Hartsough LA, Landry BP, Ekness F, Yokoo R, Gomez EJ, Ramakrishnan P, Suh J, Savage DF, Tabor JJ. An open-hardware platform for optogenetics and photobiology. Scientific Reports. 6: 35363. PMID 27805047 DOI: 10.1038/srep35363  0.48
2016 Morgan SA, Nadler DC, Yokoo R, Savage DF. Biofuel metabolic engineering with biosensors. Current Opinion in Chemical Biology. 35: 150-158. PMID 27768949 DOI: 10.1016/j.cbpa.2016.09.020  0.52
2016 Mangan NM, Flamholz A, Hood RD, Milo R, Savage DF. pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proceedings of the National Academy of Sciences of the United States of America. PMID 27551079 DOI: 10.1073/pnas.1525145113  0.32
2016 Hood RD, Higgins SA, Flamholz A, Nichols RJ, Savage DF. The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus. Proceedings of the National Academy of Sciences of the United States of America. PMID 27486247 DOI: 10.1073/pnas.1524915113  0.32
2016 Nadler DC, Morgan SA, Flamholz A, Kortright KE, Savage DF. Rapid construction of metabolite biosensors using domain-insertion profiling. Nature Communications. 7: 12266. PMID 27470466 DOI: 10.1038/ncomms12266  0.92
2016 Cassidy-Amstutz C, Oltrogge LM, Going CC, Lee A, Teng PK, Quintanilla D, East-Seletsky A, Williams ER, Savage DF. Identification of a minimal peptide tag for in vivo and in vitro loading of encapsulin. Biochemistry. PMID 27224728 DOI: 10.1021/acs.biochem.6b00294  0.92
2016 Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nature Biotechnology. 34: 646-51. PMID 27136077 DOI: 10.1038/nbt.3528  0.52
2015 Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. Programmed ribosomal frameshifting mediates expression of the α-carboxysome. Journal of Molecular Biology. PMID 26608811 DOI: 10.1016/j.jmb.2015.11.017  0.92
2015 Yokoo R, Hood RD, Savage DF. Live-cell imaging of cyanobacteria. Photosynthesis Research. 126: 33-46. PMID 25366827 DOI: 10.1007/s11120-014-0049-x  0.48
2014 Oakes BL, Nadler DC, Savage DF. Protein engineering of Cas9 for enhanced function Methods in Enzymology. 546: 491-511. PMID 25398355 DOI: 10.1016/B978-0-12-801185-0.00024-6  0.92
2014 Yokoo R, Hood RD, Savage DF. Live-cell imaging of cyanobacteria Photosynthesis Research. DOI: 10.1007/s11120-014-0049-x  0.92
2013 Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. Plos One. 8: e76127. PMID 24023971 DOI: 10.1371/journal.pone.0076127  0.92
2012 Chen AH, Afonso B, Silver PA, Savage DF. Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. Plos One. 7: e47837. PMID 23112856 DOI: 10.1371/journal.pone.0047837  0.92
2012 Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. Modularity of a carbon-fixing protein organelle. Proceedings of the National Academy of Sciences of the United States of America. 109: 478-83. PMID 22184212 DOI: 10.1073/pnas.1108557109  0.92
2010 Savage DF, O'Connell JD, Miercke LJ, Finer-Moore J, Stroud RM. Structural context shapes the aquaporin selectivity filter. Proceedings of the National Academy of Sciences of the United States of America. 107: 17164-9. PMID 20855585 DOI: 10.1073/pnas.1009864107  0.92
2010 Niederholtmeyer H, Wolfstädter BT, Savage DF, Silver PA, Way JC. Engineering cyanobacteria to synthesize and export hydrophilic products. Applied and Environmental Microbiology. 76: 3462-6. PMID 20363793 DOI: 10.1128/AEM.00202-10  0.92
2010 Savage DF, Afonso B, Chen AH, Silver PA. Spatially ordered dynamics of the bacterial carbon fixation machinery. Science (New York, N.Y.). 327: 1258-61. PMID 20203050 DOI: 10.1126/science.1186090  0.92
2009 Newby ZE, O'Connell JD, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM. A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nature Protocols. 4: 619-37. PMID 19360018 DOI: 10.1038/nprot.2009.27  0.92
2008 Savage DF, Way J, Silver PA. Defossiling fuel: how synthetic biology can transform biofuel production. Acs Chemical Biology. 3: 13-6. PMID 18205286 DOI: 10.1021/cb700259j  0.92
2007 Savage DF, Anderson CL, Robles-Colmenares Y, Newby ZE, Stroud RM. Cell-free complements in vivo expression of the E. coli membrane proteome. Protein Science : a Publication of the Protein Society. 16: 966-76. PMID 17456747 DOI: 10.1110/ps.062696307  0.92
2007 Savage DF, Stroud RM. Structural basis of aquaporin inhibition by mercury. Journal of Molecular Biology. 368: 607-17. PMID 17376483 DOI: 10.1016/j.jmb.2007.02.070  0.92
2004 Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM. Substrate twinning activates the signal recognition particle and its receptor. Nature. 427: 215-21. PMID 14724630 DOI: 10.1038/nature02250  0.92
2004 Lee JK, Khademi S, Harries W, Savage D, Miercke L, Stroud RM. Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family. Journal of Synchrotron Radiation. 11: 86-8. PMID 14646142 DOI: 10.1107/S0909049503023872  0.92
2003 Savage DF, Egea PF, Robles-Colmenares Y, O'Connell JD, Stroud RM. Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z. Plos Biology. 1: E72. PMID 14691544 DOI: 10.1371/journal.pbio.0000072  0.92
2003 Stroud RM, Savage D, Miercke LJ, Lee JK, Khademi S, Harries W. Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. Febs Letters. 555: 79-84. PMID 14630323 DOI: 10.1016/S0014-5793(03)01195-5  0.92
2003 Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJ, O'Connell JD, Khosla C, Stroud RM. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure (London, England : 1993). 11: 147-54. PMID 12575934 DOI: 10.1016/S0969-2126(03)00004-2  0.92
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